vimms/mkdocs.yml at main · glasgowcompbio/vimms · GitHub

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# mkdocs.yml
site_name: Virtual Metabolomics Mass Spectrometry (ViMMS)
site_url: https://glasgowcompbio.github.io/vimms/
site_description: ViMMS - Virtual Metabolomics Mass Spectrometry Framework
site_author: Glasgow Computational Biology Group

repo_name: glasgowcompbio/vimms
repo_url: https://github.com/glasgowcompbio/vimms
edit_uri: edit/main/docs/

theme:
  name: material
  features:
    - navigation.tabs
    - navigation.sections
    - navigation.expand
    - navigation.path
    - toc.integrate
    - search.suggest
    - search.highlight
    - content.code.annotate
    - content.code.copy
  palette:
    - scheme: default
      primary: indigo
      accent: indigo
      toggle:
        icon: material/brightness-7
        name: Switch to dark mode
    - scheme: slate
      primary: indigo
      accent: indigo
      toggle:
        icon: material/brightness-4
        name: Switch to light mode

plugins:
  - search
  - mkdocstrings:
      handlers:
        python:
          paths: ["."]
          options:
            show_source: true
            show_root_heading: true
            show_root_full_path: false
            show_symbol_type_heading: true
            show_symbol_type_toc: true
            docstring_style: google
            docstring_section_style: table
            merge_init_into_class: true
            show_if_no_docstring: false
            show_signature_annotations: true
            separate_signature: true
            line_length: 80

markdown_extensions:
  - admonition
  - codehilite:
      guess_lang: false
  - toc:
      permalink: true
  - pymdownx.superfences
  - pymdownx.details
  - pymdownx.tabbed:
      alternate_style: true

nav:
  - Home: README.md
  - User Guide:
      - Simulation Overview: simulation_overview.md
      - Creating Chemicals: chemicals.md
      - Running Controllers: controllers.md
      - Evaluating Simulations: evaluation.md
      - Running on a Real Instrument: real_instrument.md
      - Adding Noise: noise.md
      - Chromatographic Models: chromatography.md
      - Command Line Utilities: cli_tools.md
  - API Documentation:
      - Common: api/common.md
      - Chemical Generation Process:
          - Chemicals: api/chemicals.md
          - Chemical Samplers: api/chemical_samplers.md
          - ROI: api/roi.md
          - Box: api/box.md
      - Mass Spectrometry Process:
          - Mass Spec: api/mass_spec.md
          - Column: api/column.md
          - Noise: api/noise.md
      - Fragmentation Strategy Simulation Process:
          - Environment: api/environment.md
          - Controllers: api/controllers.md
          - Dynamic Exclusion: api/exclusion.md
          - Agents: api/agent.md
      - Others:
          - Feature Extractions: api/feature_extractions.md
          - MzMLWriter: api/mzml_writer.md

extra:
  social:
    - icon: fontawesome/brands/github
      link: https://github.com/glasgowcompbio/vimms
    - icon: fontawesome/solid/book
      link: https://doi.org/10.1021/acs.analchem.9b02521

copyright: Copyright &copy; 2025 Glasgow Computational Biology Group